You can just center your ensemble, then you can calculate the accurate RMSD. You know during the MD process, the molecule will also transfer moving in different time. So you have to align all these frames, before you calculate RMSD.

then I run ptraj, the last rmsd data is 4.23673, I also use "ambpdb -p m_wat.prmtop <nptm532.rst> m32.pdb" to generate the last structure m32.pdb, then I import the two structures into pymol, align m32.pdb and resi 1-104 and name c+ca+n,m_in.pdb and resi 1-104 and name c+ca+n, the calculated rmsd is 2.118. I don't know if I have described my question clearly, thank you for your attention.
2009-11-18